Bacteria may need to be characterized for a number of reasons. Newly discovered organisms are characterized to determine their taxonomic position; clinical isolates are characterized to provide an indication of pathogenic potential and likely antibiotic susceptibility. Such studies generally mvolve characterization to the genus and species level and provide an identification for the organism. Highly discrimmatory methods of intraspecies characterization are required for epidemiologic purposes in order to establish sources and routes of mfection to which control measures may be directed. For an mdlvidual patient, differentiation between relapsmg infection or reinfection may ard treatment choice and clinical management. The pattern of DNA fragments produced by digestion of genomic DNA with a restriction endonuclease, directly or after hybridization, can be highly discrimmatory and enable strain characterization, or typing, suitable for epidemiologic studies. The practice of obtaining these patterns (or profiles) for epidemiologic purposes is the subject of the present chapter, although the methods can also be applied to questions regarding identification at higher taxonomic levels.